Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/networkx/tests/test_convert_pandas.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 import pytest |
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2 import networkx as nx |
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3 from networkx.testing import assert_nodes_equal |
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4 from networkx.testing import assert_edges_equal |
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5 from networkx.testing import assert_graphs_equal |
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6 |
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7 np = pytest.importorskip("numpy") |
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8 pd = pytest.importorskip("pandas") |
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9 |
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10 |
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11 class TestConvertPandas: |
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12 def setup_method(self): |
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13 self.rng = np.random.RandomState(seed=5) |
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14 ints = self.rng.randint(1, 11, size=(3, 2)) |
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15 a = ["A", "B", "C"] |
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16 b = ["D", "A", "E"] |
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17 df = pd.DataFrame(ints, columns=["weight", "cost"]) |
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18 df[0] = a # Column label 0 (int) |
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19 df["b"] = b # Column label 'b' (str) |
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20 self.df = df |
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21 |
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22 mdf = pd.DataFrame([[4, 16, "A", "D"]], columns=["weight", "cost", 0, "b"]) |
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23 self.mdf = df.append(mdf) |
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24 |
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25 def test_exceptions(self): |
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26 G = pd.DataFrame(["a"]) # adj |
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27 pytest.raises(nx.NetworkXError, nx.to_networkx_graph, G) |
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28 G = pd.DataFrame(["a", 0.0]) # elist |
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29 pytest.raises(nx.NetworkXError, nx.to_networkx_graph, G) |
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30 df = pd.DataFrame([[1, 1], [1, 0]], dtype=int, index=[1, 2], columns=["a", "b"]) |
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31 pytest.raises(nx.NetworkXError, nx.from_pandas_adjacency, df) |
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32 |
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33 def test_from_edgelist_all_attr(self): |
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34 Gtrue = nx.Graph( |
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35 [ |
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36 ("E", "C", {"cost": 9, "weight": 10}), |
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37 ("B", "A", {"cost": 1, "weight": 7}), |
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38 ("A", "D", {"cost": 7, "weight": 4}), |
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39 ] |
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40 ) |
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41 G = nx.from_pandas_edgelist(self.df, 0, "b", True) |
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42 assert_graphs_equal(G, Gtrue) |
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43 # MultiGraph |
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44 MGtrue = nx.MultiGraph(Gtrue) |
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45 MGtrue.add_edge("A", "D", cost=16, weight=4) |
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46 MG = nx.from_pandas_edgelist(self.mdf, 0, "b", True, nx.MultiGraph()) |
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47 assert_graphs_equal(MG, MGtrue) |
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48 |
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49 def test_from_edgelist_multi_attr(self): |
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50 Gtrue = nx.Graph( |
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51 [ |
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52 ("E", "C", {"cost": 9, "weight": 10}), |
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53 ("B", "A", {"cost": 1, "weight": 7}), |
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54 ("A", "D", {"cost": 7, "weight": 4}), |
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55 ] |
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56 ) |
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57 G = nx.from_pandas_edgelist(self.df, 0, "b", ["weight", "cost"]) |
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58 assert_graphs_equal(G, Gtrue) |
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59 |
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60 def test_from_edgelist_multi_attr_incl_target(self): |
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61 Gtrue = nx.Graph( |
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62 [ |
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63 ("E", "C", {0: "C", "b": "E", "weight": 10}), |
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64 ("B", "A", {0: "B", "b": "A", "weight": 7}), |
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65 ("A", "D", {0: "A", "b": "D", "weight": 4}), |
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66 ] |
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67 ) |
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68 G = nx.from_pandas_edgelist(self.df, 0, "b", [0, "b", "weight"]) |
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69 assert_graphs_equal(G, Gtrue) |
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70 |
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71 def test_from_edgelist_multidigraph_and_edge_attr(self): |
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72 # example from issue #2374 |
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73 edges = [ |
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74 ("X1", "X4", {"Co": "zA", "Mi": 0, "St": "X1"}), |
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75 ("X1", "X4", {"Co": "zB", "Mi": 54, "St": "X2"}), |
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76 ("X1", "X4", {"Co": "zB", "Mi": 49, "St": "X3"}), |
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77 ("X1", "X4", {"Co": "zB", "Mi": 44, "St": "X4"}), |
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78 ("Y1", "Y3", {"Co": "zC", "Mi": 0, "St": "Y1"}), |
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79 ("Y1", "Y3", {"Co": "zC", "Mi": 34, "St": "Y2"}), |
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80 ("Y1", "Y3", {"Co": "zC", "Mi": 29, "St": "X2"}), |
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81 ("Y1", "Y3", {"Co": "zC", "Mi": 24, "St": "Y3"}), |
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82 ("Z1", "Z3", {"Co": "zD", "Mi": 0, "St": "Z1"}), |
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83 ("Z1", "Z3", {"Co": "zD", "Mi": 14, "St": "X3"}), |
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84 ] |
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85 Gtrue = nx.MultiDiGraph(edges) |
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86 data = { |
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87 "O": ["X1", "X1", "X1", "X1", "Y1", "Y1", "Y1", "Y1", "Z1", "Z1"], |
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88 "D": ["X4", "X4", "X4", "X4", "Y3", "Y3", "Y3", "Y3", "Z3", "Z3"], |
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89 "St": ["X1", "X2", "X3", "X4", "Y1", "Y2", "X2", "Y3", "Z1", "X3"], |
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90 "Co": ["zA", "zB", "zB", "zB", "zC", "zC", "zC", "zC", "zD", "zD"], |
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91 "Mi": [0, 54, 49, 44, 0, 34, 29, 24, 0, 14], |
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92 } |
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93 df = pd.DataFrame.from_dict(data) |
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94 G1 = nx.from_pandas_edgelist( |
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95 df, source="O", target="D", edge_attr=True, create_using=nx.MultiDiGraph |
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96 ) |
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97 G2 = nx.from_pandas_edgelist( |
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98 df, |
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99 source="O", |
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100 target="D", |
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101 edge_attr=["St", "Co", "Mi"], |
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102 create_using=nx.MultiDiGraph, |
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103 ) |
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104 assert_graphs_equal(G1, Gtrue) |
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105 assert_graphs_equal(G2, Gtrue) |
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106 |
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107 def test_from_edgelist_one_attr(self): |
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108 Gtrue = nx.Graph( |
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109 [ |
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110 ("E", "C", {"weight": 10}), |
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111 ("B", "A", {"weight": 7}), |
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112 ("A", "D", {"weight": 4}), |
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113 ] |
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114 ) |
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115 G = nx.from_pandas_edgelist(self.df, 0, "b", "weight") |
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116 assert_graphs_equal(G, Gtrue) |
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117 |
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118 def test_from_edgelist_int_attr_name(self): |
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119 # note: this also tests that edge_attr can be `source` |
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120 Gtrue = nx.Graph( |
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121 [("E", "C", {0: "C"}), ("B", "A", {0: "B"}), ("A", "D", {0: "A"})] |
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122 ) |
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123 G = nx.from_pandas_edgelist(self.df, 0, "b", 0) |
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124 assert_graphs_equal(G, Gtrue) |
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125 |
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126 def test_from_edgelist_invalid_attr(self): |
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127 pytest.raises( |
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128 nx.NetworkXError, nx.from_pandas_edgelist, self.df, 0, "b", "misspell" |
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129 ) |
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130 pytest.raises(nx.NetworkXError, nx.from_pandas_edgelist, self.df, 0, "b", 1) |
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131 # see Issue #3562 |
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132 edgeframe = pd.DataFrame([[0, 1], [1, 2], [2, 0]], columns=["s", "t"]) |
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133 pytest.raises( |
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134 nx.NetworkXError, nx.from_pandas_edgelist, edgeframe, "s", "t", True |
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135 ) |
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136 pytest.raises( |
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137 nx.NetworkXError, nx.from_pandas_edgelist, edgeframe, "s", "t", "weight" |
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138 ) |
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139 pytest.raises( |
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140 nx.NetworkXError, |
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141 nx.from_pandas_edgelist, |
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142 edgeframe, |
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143 "s", |
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144 "t", |
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145 ["weight", "size"], |
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146 ) |
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147 |
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148 def test_from_edgelist_no_attr(self): |
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149 Gtrue = nx.Graph([("E", "C", {}), ("B", "A", {}), ("A", "D", {})]) |
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150 G = nx.from_pandas_edgelist(self.df, 0, "b") |
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151 assert_graphs_equal(G, Gtrue) |
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152 |
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153 def test_from_edgelist(self): |
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154 # Pandas DataFrame |
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155 G = nx.cycle_graph(10) |
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156 G.add_weighted_edges_from((u, v, u) for u, v in list(G.edges)) |
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157 |
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158 edgelist = nx.to_edgelist(G) |
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159 source = [s for s, t, d in edgelist] |
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160 target = [t for s, t, d in edgelist] |
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161 weight = [d["weight"] for s, t, d in edgelist] |
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162 edges = pd.DataFrame({"source": source, "target": target, "weight": weight}) |
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163 |
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164 GG = nx.from_pandas_edgelist(edges, edge_attr="weight") |
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165 assert_nodes_equal(G.nodes(), GG.nodes()) |
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166 assert_edges_equal(G.edges(), GG.edges()) |
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167 GW = nx.to_networkx_graph(edges, create_using=nx.Graph) |
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168 assert_nodes_equal(G.nodes(), GW.nodes()) |
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169 assert_edges_equal(G.edges(), GW.edges()) |
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170 |
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171 def test_to_edgelist_default_source_or_target_col_exists(self): |
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172 |
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173 G = nx.path_graph(10) |
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174 G.add_weighted_edges_from((u, v, u) for u, v in list(G.edges)) |
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175 nx.set_edge_attributes(G, 0, name="source") |
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176 pytest.raises(nx.NetworkXError, nx.to_pandas_edgelist, G) |
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177 |
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178 # drop source column to test an exception raised for the target column |
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179 for u, v, d in G.edges(data=True): |
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180 d.pop("source", None) |
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181 |
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182 nx.set_edge_attributes(G, 0, name="target") |
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183 pytest.raises(nx.NetworkXError, nx.to_pandas_edgelist, G) |
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184 |
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185 def test_to_edgelist_custom_source_or_target_col_exists(self): |
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186 |
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187 G = nx.path_graph(10) |
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188 G.add_weighted_edges_from((u, v, u) for u, v in list(G.edges)) |
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189 nx.set_edge_attributes(G, 0, name="source_col_name") |
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190 pytest.raises( |
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191 nx.NetworkXError, nx.to_pandas_edgelist, G, source="source_col_name" |
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192 ) |
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193 |
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194 # drop source column to test an exception raised for the target column |
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195 for u, v, d in G.edges(data=True): |
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196 d.pop("source_col_name", None) |
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197 |
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198 nx.set_edge_attributes(G, 0, name="target_col_name") |
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199 pytest.raises( |
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200 nx.NetworkXError, nx.to_pandas_edgelist, G, target="target_col_name" |
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201 ) |
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202 |
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203 def test_from_adjacency(self): |
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204 nodelist = [1, 2] |
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205 dftrue = pd.DataFrame( |
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206 [[1, 1], [1, 0]], dtype=int, index=nodelist, columns=nodelist |
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207 ) |
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208 G = nx.Graph([(1, 1), (1, 2)]) |
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209 df = nx.to_pandas_adjacency(G, dtype=int) |
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210 pd.testing.assert_frame_equal(df, dftrue) |
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211 |
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212 def test_roundtrip(self): |
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213 # edgelist |
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214 Gtrue = nx.Graph([(1, 1), (1, 2)]) |
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215 df = nx.to_pandas_edgelist(Gtrue) |
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216 G = nx.from_pandas_edgelist(df) |
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217 assert_graphs_equal(Gtrue, G) |
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218 # adjacency |
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219 adj = {1: {1: {"weight": 1}, 2: {"weight": 1}}, 2: {1: {"weight": 1}}} |
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220 Gtrue = nx.Graph(adj) |
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221 df = nx.to_pandas_adjacency(Gtrue, dtype=int) |
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222 G = nx.from_pandas_adjacency(df) |
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223 assert_graphs_equal(Gtrue, G) |
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224 |
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225 def test_from_adjacency_named(self): |
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226 # example from issue #3105 |
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227 data = { |
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228 "A": {"A": 0, "B": 0, "C": 0}, |
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229 "B": {"A": 1, "B": 0, "C": 0}, |
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230 "C": {"A": 0, "B": 1, "C": 0}, |
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231 } |
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232 dftrue = pd.DataFrame(data) |
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233 df = dftrue[["A", "C", "B"]] |
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234 G = nx.from_pandas_adjacency(df, create_using=nx.DiGraph()) |
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235 df = nx.to_pandas_adjacency(G, dtype=np.intp) |
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236 pd.testing.assert_frame_equal(df, dftrue) |
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237 |
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238 def test_edgekey_with_multigraph(self): |
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239 df = pd.DataFrame( |
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240 { |
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241 "attr1": {"A": "F1", "B": "F2", "C": "F3"}, |
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242 "attr2": {"A": 1, "B": 0, "C": 0}, |
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243 "attr3": {"A": 0, "B": 1, "C": 0}, |
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244 "source": {"A": "N1", "B": "N2", "C": "N1"}, |
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245 "target": {"A": "N2", "B": "N3", "C": "N1"}, |
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246 } |
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247 ) |
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248 Gtrue = nx.Graph( |
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249 [ |
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250 ("N1", "N2", {"F1": {"attr2": 1, "attr3": 0}}), |
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251 ("N2", "N3", {"F2": {"attr2": 0, "attr3": 1}}), |
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252 ("N1", "N1", {"F3": {"attr2": 0, "attr3": 0}}), |
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253 ] |
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254 ) |
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255 # example from issue #4065 |
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256 G = nx.from_pandas_edgelist( |
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257 df, |
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258 source="source", |
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259 target="target", |
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260 edge_attr=["attr2", "attr3"], |
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261 edge_key="attr1", |
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262 create_using=nx.MultiGraph(), |
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263 ) |
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264 assert_graphs_equal(G, Gtrue) |
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265 |
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266 def test_edgekey_with_normal_graph_no_action(self): |
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267 Gtrue = nx.Graph( |
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268 [ |
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269 ("E", "C", {"cost": 9, "weight": 10}), |
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270 ("B", "A", {"cost": 1, "weight": 7}), |
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271 ("A", "D", {"cost": 7, "weight": 4}), |
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272 ] |
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273 ) |
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274 G = nx.from_pandas_edgelist(self.df, 0, "b", True, edge_key="weight") |
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275 assert_graphs_equal(G, Gtrue) |
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276 |
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277 def test_nonexisting_edgekey_raises(self): |
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278 with pytest.raises(nx.exception.NetworkXError): |
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279 nx.from_pandas_edgelist( |
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280 self.df, |
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281 source="source", |
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282 target="target", |
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283 edge_key="Not_real", |
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284 edge_attr=True, |
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285 create_using=nx.MultiGraph(), |
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286 ) |